SMTL ID : 6khj.1

Supercomplex for electron transfer

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

2 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)

DGD.1: 27 residues within 4Å: Chain A: D.6, L.7, Q.8, W.29, L.32, P.33, L.35, M.36, M.37, V.40, V.43, G.44, V.47, F.119, N.122, L.123, L.124, I.125, S.126, N.127, V.266, I.311, L.315 Chain C: Y.21 Chain L: Y.20, T.52 Ligands: DGD.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.7, A:L.35, A:M.36, A:V.40, A:V.43, A:V.47, A:F.119, A:F.119, A:V.266, A:I.311, A:L.315 Hydrogen bonds: A:D.6, A:Q.8, A:W.29, A:N.127 DGD.2: 25 residues within 4Å: Chain A: I.5, D.6, L.7, M.36, I.39, G.120, Q.121, N.122, L.123, W.280, L.286, Q.303, I.304, F.306, A.307, V.308, I.311 Chain L: Y.13, L.16, A.17, L.19, Y.20, F.53, P.56 Ligands: DGD.1 22 PLIP interactions: 10 interactions with chain A, 12 interactions with chain L Hydrophobic interactions: A:I.39, A:V.308, A:V.308, A:I.311, A:I.311, L:Y.13, L:L.16, L:L.16, L:A.17, L:L.19, L:Y.20, L:Y.20, L:Y.20, L:F.53, L:F.53, L:P.56 Hydrogen bonds: A:Q.121, A:N.122, A:W.280, A:Q.303, A:F.306, L:Y.13

1 x PL9: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE(Non-covalent)

PL9.3: 10 residues within 4Å: Chain A: A.237, R.329 Chain H: P.20, S.21, Q.128, F.131 Chain K: M.47, I.61, P.74, N.76 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain A, 2 interactions with chain H Hydrophobic interactions: K:I.61, A:A.237, H:F.131, H:F.131

3 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)

SQD.4: 24 residues within 4Å: Chain B: L.416, V.419, I.420, Y.423, K.430 Chain D: Q.163, Y.164, T.167, K.168, L.171, Y.172, G.175, S.176, F.179, V.220, P.230, L.231 Chain F: V.609, V.612, V.613, T.616, G.617, T.620, M.621 11 PLIP interactions: 2 interactions with chain F, 5 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: F:V.609, F:T.620, D:K.168, D:L.171, D:Y.172, D:F.179, D:V.220, B:L.416, B:I.420 Hydrogen bonds: B:Y.423 Salt bridges: B:K.430 SQD.5: 19 residues within 4Å: Chain A: K.26, L.27, L.30 Chain C: F.14, V.15, S.17, Y.19, E.20, F.22, L.23, G.24 Chain G: L.3, A.4, T.7, Q.8, T.11, L.15, G.48, I.51 14 PLIP interactions: 7 interactions with chain C, 2 interactions with chain A, 5 interactions with chain G Hydrophobic interactions: C:F.14, C:F.22, C:F.22, C:L.23, A:L.30, G:T.7, G:T.11, G:L.15, G:I.51 Hydrogen bonds: C:F.14, C:S.17, C:S.17, G:Q.8 Salt bridges: A:K.26 SQD.20: 17 residues within 4Å: Chain A: L.74, L.77 Chain K: D.33, V.34, W.37 Chain L: P.63, I.65, N.66, R.68 Chain N: G.2, L.3, L.4, P.24, F.29, R.32, V.137, V.138 11 PLIP interactions: 3 interactions with chain K, 3 interactions with chain N, 2 interactions with chain A, 3 interactions with chain L Hydrophobic interactions: K:D.33, K:V.34, K:W.37, N:L.4, A:L.74, A:L.77 Hydrogen bonds: N:V.138, L:I.65 Salt bridges: N:R.32, L:R.68, L:R.68

6 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)

LHG.6: 9 residues within 4Å: Chain A: P.350 Chain B: L.30, I.34 Chain C: V.121, W.124, R.125, R.127, E.130 Ligands: LHG.16 9 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: C:W.124, C:W.124, C:W.124, B:L.30, B:I.34, A:P.350 Salt bridges: C:R.125, C:R.125, C:R.127 LHG.7: 17 residues within 4Å: Chain B: Y.366, Q.367, P.370, T.373, L.374, S.377, L.378, P.388, S.472 Chain D: P.22, L.111, K.112, P.113, R.114, L.115, F.118, I.148 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:F.118, D:F.118, D:I.148, B:L.374, B:L.374, B:L.378, B:P.388, B:P.388 Hydrogen bonds: D:R.114, D:L.115, B:Y.366 LHG.12: 15 residues within 4Å: Chain D: F.97, P.461, V.464, F.465, A.468, C.469, V.472 Chain F: F.24, A.28, F.29, E.31 Chain P: A.13, M.14, L.21, F.25 11 PLIP interactions: 6 interactions with chain D, 3 interactions with chain P, 2 interactions with chain F Hydrophobic interactions: D:F.97, D:F.97, D:P.461, D:V.464, D:F.465, D:V.472, P:F.25, P:F.25, F:F.24, F:A.28 Hydrogen bonds: P:R.28 LHG.14: 17 residues within 4Å: Chain D: Y.297, I.432, S.436, R.439 Chain F: E.173, Q.176, K.177, V.180, T.181, V.184, P.245, L.246, Y.586, F.590, I.591, R.595 Ligands: BCR.10 19 PLIP interactions: 4 interactions with chain D, 15 interactions with chain F Hydrophobic interactions: D:I.432, F:V.184, F:P.245, F:L.246, F:Y.586, F:Y.586, F:F.590, F:F.590, F:F.590, F:F.590, F:I.591 Hydrogen bonds: D:Y.297, D:R.439, F:E.173, F:E.173, F:Q.176, F:Q.176 Salt bridges: D:R.439, F:R.595 LHG.15: 11 residues within 4Å: Chain F: Q.6, W.9, P.12, V.13, L.16, Q.71, G.86, Y.87, V.140, Q.146, F.150 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:W.9, F:W.9, F:W.9, F:P.12, F:L.16, F:Y.87, F:V.140, F:F.150 Hydrogen bonds: F:Q.6 LHG.16: 12 residues within 4Å: Chain A: I.221, D.342, K.346, F.347, P.350 Chain C: W.124 Chain I: Q.6, Y.10, E.13, A.14, S.17 Ligands: LHG.6 8 PLIP interactions: 5 interactions with chain I, 1 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: I:Y.10, I:Y.10, I:Y.10, I:E.13, I:A.14, A:P.350, C:W.124, C:W.124

2 x BCR: BETA-CAROTENE(Non-covalent)

BCR.8: 21 residues within 4Å: Chain D: L.93, F.97, A.377, M.378, A.381, A.468, L.471, V.472, P.473, I.475, G.476, I.477, L.483, L.484 Chain F: L.20, I.27 Chain P: V.7, I.10, L.11, M.14 Ligands: LMG.11 14 PLIP interactions: 10 interactions with chain D, 3 interactions with chain P, 1 interactions with chain F Hydrophobic interactions: D:L.93, D:F.97, D:A.381, D:A.468, D:L.471, D:V.472, D:I.475, D:I.475, D:I.477, D:L.483, P:V.7, P:I.10, P:L.11, F:L.20 BCR.10: 18 residues within 4Å: Chain D: V.287, I.290, Y.291, L.294, F.421, L.422, V.425 Chain F: F.187, L.235, V.238, P.245, L.246, T.297, V.601 Chain Q: I.28, F.31, I.32 Ligands: LHG.14 14 PLIP interactions: 9 interactions with chain D, 4 interactions with chain F, 1 interactions with chain Q Hydrophobic interactions: D:V.287, D:I.290, D:I.290, D:Y.291, D:L.294, D:F.421, D:F.421, D:L.422, D:V.425, F:F.187, F:V.238, F:L.246, F:V.601, Q:F.31

1 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.9: 3 residues within 4Å: Chain D: P.22, F.23, R.114 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.23, D:F.23 Hydrogen bonds: D:I.24

2 x LMG: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE(Non-covalent)

LMG.11: 20 residues within 4Å: Chain D: K.373, F.376, A.377, T.380, L.384, M.392 Chain F: A.19, L.20, G.23, L.26, P.119, G.120, R.123, Y.127, L.130, L.153, M.156, L.160, Y.166 Ligands: BCR.8 14 PLIP interactions: 13 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:A.19, F:L.20, F:L.26, F:L.130, F:L.153, F:L.160, F:L.160, D:L.384 Hydrogen bonds: F:R.123, F:Y.127, F:Y.166, F:Y.166 Salt bridges: F:R.123, F:R.123 LMG.13: 21 residues within 4Å: Chain F: F.303, T.307, I.310, T.311, N.313, L.441, F.444, R.448, M.452, V.550, M.554, Y.555, P.562, Q.563, I.565, A.566, L.572, Y.573, F.575, S.576, W.580 20 PLIP interactions: 20 interactions with chain F Hydrophobic interactions: F:F.303, F:F.303, F:T.307, F:L.441, F:F.444, F:F.444, F:F.444, F:V.550, F:I.565, F:L.572, F:L.572, F:F.575, F:W.580, F:W.580 Hydrogen bonds: F:N.313, F:R.448, F:R.448, F:Y.555, F:Y.555, F:S.576

3 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.17: 12 residues within 4Å: Chain I: I.56, C.73, P.74, L.77, P.78, C.103, I.104, F.105, C.106, A.107, N.108, C.109 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.73, I:C.103, I:C.106, I:C.109 SF4.18: 11 residues within 4Å: Chain I: C.63, I.64, C.66, V.68, C.69, Y.112, C.113, P.114, T.115, C.117, L.118 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.63, I:C.66, I:C.69, I:C.113 SF4.19: 11 residues within 4Å: Chain H: R.69, I.154 Chain K: A.51, C.52, C.53, G.88, T.89, A.116, C.117, C.148, P.149 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.52, K:C.53, K:C.117, K:C.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, X. et al., Structural basis for electron transport mechanism of complex I-like photosynthetic NAD(P)H dehydrogenase. Nat Commun (2020)

Release Date

2020-02-12

Peptides

NAD(P)H-quinone oxidoreductase subunit 1: A
NAD(P)H-quinone oxidoreductase subunit 2: B
NAD(P)H-quinone oxidoreductase subunit 3: C
NAD(P)H-quinone oxidoreductase chain 4 1: D
NAD(P)H-quinone oxidoreductase subunit 4L: E
NADH dehydrogenase subunit 5: F
NADH-quinone oxidoreductase subunit J: G
NAD(P)H-quinone oxidoreductase subunit H: H
NAD(P)H-quinone oxidoreductase subunit I: I
NAD(P)H-quinone oxidoreductase subunit J: J
NAD(P)H-quinone oxidoreductase subunit K: K
NAD(P)H-quinone oxidoreductase subunit L: L
NAD(P)H-quinone oxidoreductase subunit M: M
NAD(P)H-quinone oxidoreductase subunit N: N
NAD(P)H-quinone oxidoreductase subunit O: O
proton-translocating NADH-quinone dehydrogenase subunit P: P
proton-translocating NADH-quinone dehydrogenase subunit Q: Q
Tlr0636 protein: R

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
S

Membrane

We predict this structure to be a membrane protein.
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NAD(P)H-quinone oxidoreductase subunit 1

NAD(P)H-quinone oxidoreductase subunit 2

NAD(P)H-quinone oxidoreductase subunit 3

NAD(P)H-quinone oxidoreductase chain 4 1

NAD(P)H-quinone oxidoreductase subunit 4L

NADH dehydrogenase subunit 5

NADH-quinone oxidoreductase subunit J

NAD(P)H-quinone oxidoreductase subunit H

NAD(P)H-quinone oxidoreductase subunit I

NAD(P)H-quinone oxidoreductase subunit J

NAD(P)H-quinone oxidoreductase subunit K

NAD(P)H-quinone oxidoreductase subunit L

NAD(P)H-quinone oxidoreductase subunit M

NAD(P)H-quinone oxidoreductase subunit N

NAD(P)H-quinone oxidoreductase subunit O

proton-translocating NADH-quinone dehydrogenase subunit P

proton-translocating NADH-quinone dehydrogenase subunit Q

Tlr0636 protein

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